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Table 3 Results displaying the VAF percentages of amplicon NGS and ddPCR analyses performed on different somatic tissue samples from parents suspected of low-level mosaicism

From: Detection of low-level parental somatic mosaicism for clinically relevant SNVs and indels identified in a large exome sequencing dataset

Parent Gene Variant Blood Buccal Saliva Urine Hair Nails
ES (%) PCR NGS (%) ddPCR PCR NGS ddPCR PCR NGS ddPCR PCR NGS ddPCR PCR NGS PCR NGS
M1 USP7 c.238A > T 3 9 2.13% 1% 0.3% 8% 4.78% 2% 0.86% 0.03% 5%
M2 PTPN11 c.923A > G 1 0.3 ND 0.21% ND 0.1% NT 0.22% NT 0.15% NA
M3 PTPN11 c.923A > G 1 0.3 DEG 0.2% ND 0.2% NT 0.2% NT NA NA
M4 COL11A1 c.3816 + 2dupT 2.8 0.2 (HC) ND ND ND ND DEG ND ND ND ND
M5 CACNA1C c.694G > C 1 2 ND ND ND ND 0.2% ND 0.2% 0.05% ND
  1. HC GATK haplotype caller, NA not accountable, ND not detectable, NT not tested, DEG degraded DNA
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Human Genomics

ISSN: 1479-7364